We followed the intro SCITAS Course to connect to the Clusters Documentation is here: https://scitas-data.epfl.ch/public/training/using_the_clusters.pdf command idto know to which group you belong https://scitas-data.epfl.ch/kb/File+systems to get some information on FIleSystem =Structure of cluster = `/home/username` your personal area, shared among all 3 clusters `/work/biop` where biop sofware will be installed, shared among all 3 cluster `/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to =How to connect= =How to install software= =How to install software at the BIOP account= =How to launch a job= =Example Ilastik Launch= =Example CellProfiler Launch= =Example Fiji Launch=

We followed the intro SCITAS Course to connect to the Clusters Documentation is here: https://scitas-data.epfl.ch/public/training/using_the_clusters.pdf command id to know to which group you belong https://scitas-data.epfl.ch/kb/File+systems to get some information on FIleSystem =Structure of cluster = `/home/username` your personal area, shared among all 3 clusters `/work/ptbiop` where biop software are installed, shared among all 3 clusters `/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to =How to connect= Type `ssh gasparlogin@clustername.epfl.ch` and give your password. For instance if Nico wants to connect to the deneb1 cluster (there's also deneb2 and fidis) : `ssh chiarutt@deneb1.epfl.ch`. =How to transfer data into the server= == Windows users == == Linux users == =How to install software= You can install either software (unix executable / java applications) into your folder. =How to install software within your folder = =How to install software within the BIOP work folder = =How to launch a job= == Example Ilastik Launch == == Example CellProfiler Launch == == Example Fiji Launch ==

We followed the intro SCITAS Course to connect to the Clusters Documentation is here: https://scitas-data.epfl.ch/public/training/using_the_clusters.pdf command idto to know to which group you belong https://scitas-data.epfl.ch/kb/File+systems to get some information on FIleSystem =Structure of cluster = `/home/username` your personal area, shared among all 3 clusters `/work/ptbiop` where biop software will bare installed, shared among all 3 clusters `/scratch/username` is a high performance file system where we put the data we need to work on, it is not shared and depends on the cluster you are connected to =How to connect= Type `ssh gasparlogin@clustername.epfl.ch` and give your password. For instance if Nico wants to connect to the deneb1 cluster (there's also deneb2 and fidis) : `ssh chiarutt@deneb1.epfl.ch`. =How to transfer data into the server= =How to connect=== Windows users == == Linux users == =How to install software= You can install either software (unix executable / java applications) into your folder. =How to install software within your folder = =How to install software atwithin the BIOP account=work folder = =How to launch a job= === Example Ilastik Launch= = == == Example CellProfiler Launch= = == == Example Fiji Launch= ==